Cutting a deal with the alleged Boston bomber might prevent future attacks and ensure a conviction. But it could enrage victims and disappoint the public.

America’s two most brutal terrorists met the same fate they brought about for so many others. Oklahoma City bomber Timothy McVeigh died in a federal prison, Osama bin Laden in a Pakistani safe house. Both deaths were welcomed by a relieved American public.

By and large, however, that hasn’t been the way the U.S. government has punished those who have masterminded terrorist attacks on home soil. Today, the Unabomber, Theodore Kaczynski, sits in a supermax cell in Colorado, as does Eric Rudolph, who detonated a bomb during the 1996 Summer Olympics in Atlanta. Both were domestic terrorists who killed a handful of people in crimes similar to those Dzhokhar Tsarnaev is accused of committing in Boston. In that same prison, too, is Zacarias Moussaoui, the “20th hijacker” who was convicted in the 9/11 attacks. All three were eligible for the death penalty, and all three will likely die in prison. But it won’t be via lethal injection.

With investigators still looking to connect Tsarnaev and his late brother, Tamerlan, to overseas provocateurs, the debate over whether federal prosecutors should seek the death penalty for Dzhokhar is just beginning to rage. The prospect promises to put the Justice Department, and the Obama administration as a whole, in a tight spot, where the desire to punish Tsarnaev to the limit comes up against the pragmatics of the criminal-justice system.

And should agents suspect links between the Tsarnaevs and a foreign terrorist network or should more accomplices come to light, the pressure to seek a plea, to use the threat of the needle to push Dzhokhar to “flip” and provide information to the government, will intensify, even as will the cries for his head.

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In other contexts, there wouldn’t be much of a choice, but terrorism is different, because the overall mission of the government—prosecutors and all—is “to protect the country from future attacks,” says Daniel Collins, a former federal prosecutor in Chicago. As an assistant U.S. attorney, Collins secured a guilty plea from David Headley, a Pakistani-American implicated in the Mumbai, India, bombings of 2008. After Headley agreed to cooperate, he was ultimately given 35 years in prison, a sentence that drew criticism. “Taking the death penalty off the table is no small decision,” Collins says.

There are other reasons prosecutors could seek a deal. This week, Tsarnaev added defense attorney Judy Clarke, known for helping her clients avoid execution, to his team. She represented both Kaczynski and Rudolph, as well as Susan Smith, the South Carolina mother who drowned her two children, and Jared Loughner, who pleaded guilty to the Tucson, Ariz., massacre that gravely wounded then-Rep. Gabrielle Giffords. In a recent speech, as reported by the Associated Press, Clarke said her task is to persuade her clients to plead guilty to save their lives. “Our job is to provide them with a reason to live,” she said.

Before Tsarnaev ever reaches that stage, however, the Justice Department will have to approve the prosecution as a capital case. According to guidelines released by Attorney General Eric Holder in 2011, the government can’t seek the death penalty simply to gain negotiating leverage. It must also consult with the families of the victims before issuing a ruling.

Still, observers widely expect Justice to green-light a capital case. And Collins believes Clarke could have a tough time of it because of the trove of evidence and the fact that Tsarnaev has already implicated himself. For that reason, some lawyers, such as William Otis, a former counsel to President George W. Bush, believe the government shouldn’t be quick to cut a deal. Tsarnaev needs to face a jury, Otis wrote for Forbes this week, with death on the line. “Vengeance is hardly the only reason people of good faith support the death penalty in extreme cases,” he asserted, noting that polls showed 80 percent of the American public favored McVeigh’s execution. “Wanting justice is not wanting vengeance.”

Douglas Berman, a professor at the Ohio State University Moritz College of Law, isn’t so sure the government won’t want to strike a bargain if Clarke begins to punch holes in its case and threatens to turn a trial (and the inevitable appeals) into a lengthy spectacle. “The prosecution’s case is as good right now as it is ever going to be,” he says, “and the defense is just getting revved up.”

Berman says the case raises the question, “Whose interest can and should a prosecutor be thinking about serving: the interests of the United States of America, whatever that means? The interests of the citizens of Boston? What does it mean to serve justice?”

In Kaczynski’s case, justice meant denying him a public trial that would serve as a platform for his antigovernment views. In Rudolph’s, it meant getting information to locate dynamite he had hidden away in the North Carolina mountains. After convicting Moussaoui, a jury sentenced him to life in prison rather than the execution chamber. Sparing him, Judge Leonie Brinkema said at the time, denied him “martyrdom in a great big bang of glory.”

It’s entirely possible that Tsarnaev’s prosecutors could decide, at some point, it may be more inflammatory to kill him than imprison him. That will be a concern, along with the need to gather intelligence, questions about evidence, and the merits of Dzhokhar’s defense. Ultimately, if Justice makes the call to lock down a conviction rather than execute him, the victims and the public alike will demand an explanation. And the White House may find itself yet again defending its decision to try a terrorist in open court. It’s a place where things quickly grow complicated.